ecosim.in

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Sediment Model Input Script - ecosim.in

The ecosim.in file sets the parameters for the EcoSim model. The name of this file is set by the BPARNAM keyword in the ocean.in file. A default ecosim.in standard input ASCII file can be found in the User/External subdirectory of the ROMS source code. In order to include the EcoSim model in ROMS you must set BPARNAM correctly and activate the ECOSIM CPP option.


Note Notice: Detailed information about ROMS input script file syntax can be found here.


Biological Model Control Parameters

  • This switch to control the computation of EcoSim within nested and/or multiple connected grids.
Lbiology == T
  • Maximum number of iterations to achieve convergence of the nonlinear solution.
BioIter == 1
  • Calculation control switches.
RtUVR_flag == T  ! calculate CDOC UV photolysis
NFIX_flag == F  ! calculate temperature based nitrogen fixation
Regen_flag == T  ! calculate fecal matter regeneration

Phytoplankton Group Parameters

  • Unless specified, [1:Nphy,1:Ngrids] values are expected for each parameter. This file is configured for Nphy=1 and Ngrids=1. The order of phytoplankton are:
    1. larger diatoms
    2. small diatoms
    3. dinoflagellates
    4. synechococcus.
  • Half-saturation for phytoplankton NO3 uptake (micromole_NO3/liter).
HsNO3 == 8.2400d-01 4.1200d-01 8.2400d-01 1.6700d-01
  • Half-saturation for phytoplankton NH4 uptake (micromole_NH4/liter).
HsNH4 == 4.1400d-01 2.0800d-01 4.1400d-01 8.3000d-02
  • Half-saturation for phytoplankton SiO uptake (micromole_SiO/liter). A value of 1.0d+30 denotes no SiO uptake being calculated for that phytoplankton group.
HsSiO == 1.8240d+00 1.4120d+00 1.0000d+30 1.0000d+30
  • Half-saturation for phytoplankton PO4 uptake (micromole_PO4/liter)
HsPO4 == 5.1500d-02 2.5750d-02 5.1500d-02 1.0438d-02
  • Half-saturation for phytoplankton Fe uptake (micromole_Fe/liter). A value of 1.0d+30 denotes no Fe uptake being calculated for that phytoplankton group.
HsFe == 1.0000d+30 1.0000d+30 1.0000d+30 1.0000d+30
  • Maximum phytoplankton 24 hour growth rate (1/d).
GtALG_max == 3.7000d+00 3.7000d+00 2.0000d+00 2.0000d+00
  • Phytoplankton temperature base for exponential response to temperature (Celsius).
PhyTbase == 4*27.0d0
  • Phytoplankton exponential temperature factor (1/Celsius).
PhyTfac == 4*0.0633d0
  • Nitrate uptake inhibition for NH4 (1/micromole).
BET_ == 1.2800d+00 2.6000d+00 1.2800d+00 6.5000d+00
  • Maximum phytoplankton C:N ratio (micromole_C/micromole_N).
maxC2nALG == 1.4000d+01 1.7750d+01 1.7000d+01 6.6250d+00
  • Balanced phytoplankton C:N ratio (micromole_C/micromole_N).
minC2nALG == 6.6250d+00 6.6250d+00 6.6250d+00 6.6250d+00
  • Absolute minimum phytoplankton C:N ratio (micromole_C/micromole_N).
C2nALGminABS == 5.5000d+00 5.5000d+00 5.5000d+00 5.5000d+00
  • Maximum phytoplankton C:Si ratio (micromole_C/micromole_Si). A value of 0.0 denotes no silica used.
maxC2SiALG == 5.5210d+00 5.5210d+00 0.0000d+00 0.0000d+00
  • Balanced phytoplankton C:Si ratio (micromole_C/micromole_Si). A value of 1.0 denotes no silica used.
minC2SiALG == 5.5210d+00 5.5210d+00 1.0000d+00 1.0000d+00
  • Absolute minimum phytoplankton C:Si ratio (micromole_C/micromole_Si). A value of 1.0 denotes no silica used.
C2SiALGminABS == 4.5831d+00 4.5831d+00 1.0000d+00 1.0000d+00
  • Maximum phytoplankton C:P ratio (micromole_C/micromole_P). A value of 1.0 denotes no silica used.
maxC2pALG == 1.0600d+02 1.0600d+02 1.3000d+02 1.0600d+02
  • Balanced phytoplankton C:P ratio (micromole_C/micromole_P).
minC2pALG == 1.0600d+02 1.0600d+02 1.0600d+02 1.0600d+02
  • Absolute minimum phytoplankton C:P ratio (micromole_C/micromole_P).
C2pALGminABS == 8.800d+01 8.800d+01 8.800d+01 8.800d+01
  • Maximum phytoplankton C:Fe ratio (micromole_C/micromole_Fe). A value of 1.0d+30 denotes no Fe uptake being calculated.
maxC2FeALG == 1.0000d+30 1.0000d+30 1.0000d+30 1.0000d+30
  • Balanced phytoplankton C:Fe ratio (micromole_C/micromole_Fe). A value of 1.0d+30 denotes no Fe uptake being calculated.
minC2FeALG == 1.0000d+30 1.0000d+30 1.0000d+30 1.0000d+30
  • Absolute minimum phytoplankton C:Fe ratio (micromole_C/micromole_Fe). A value of 1.0d+30 denotes no Fe uptake being calculated.
C2FeALGminABS == 1.0000d+30 1.0000d+30 1.0000d+30 1.0000d+30
  • Maximum quantum yield (micromole_C/micromole_quanta).
qu_yld == 8.3300d-02 8.3300d-02 8.3300d-02 8.3300d-02
  • Compensation light level (micromole_quanta).
E0_comp == 1.0000d+01 1.0000d+01 1.0000d+01 6.0000d+00
  • Light level for onset of photoinhibition (micromole_quanta).
E0_inhib == 1.0000d+04 1.0000d+04 1.0500d+02 1.0000d+04
  • Exponential decay factor for light limited growth (1/micromole_quanta).
inhib_fac == 0.0000d+00 0.0000d+00 1.0000d-03 0.0000d+00
  • Maximum lighted limited (nutrient replete) C:Chl ratio (microgram_C/microgram_Chl).
C2CHL_max == 6.0000d+01 4.2000d+01 1.2400d+02 1.6000d+02
  • Rate of change in light limited C:Chl ratio (microgram_C/microgram_Chl/micromole_quanta).
mxC2Cl == 1.2000d-01 1.1440d-01 4.7790d-01 1.0000d-01
  • Minimum lighted limited (nutrient replete) C:Chl ratio (microgram_C/microgram_Chl)
b_C2Cl == 2.5000d+01 1.4800d+01 4.7530d+01 3.0000d+01
  • Rate of change in nutient limited C:Chl ratio [(microgram_C/microgram_Chl)/(micromole_C/micromole_N)]. A value of 0.0 denotes no change in C:Chl with nutrient status.
mxC2Cn == 1.2200d+01 6.8315d+00 1.0350d+01 0.0000d+00
  • Minimum nutrient limited C:Chl ratio (microgram_C/microgram_Chl). A value of 0.0 denotes no change in C:Chl with nutrient status.
b_C2Cn == 6.0000d+01 4.2000d+01 1.2400d+02 0.0000d+00
  • Rate of change in package effect [1/(microgram_C/microgram_Chl)]. A value of 0.0 denotes no change in package effect.
mxPacEff == 1.4290d-02 1.8380d-02 0.0000d+00 0.0000d+00
  • Maximum package effect [1/(microgram_C/microgram_Chl)]. A value of 0.0 denotes no change in package effect.
b_PacEff == 5.0000d-01 5.0000d-01 0.0000d+00 0.0000d+00
  • Rate of change in the Chl_b:Chl_a ratio [(microgram_Chl_b/microgram_Chl_a)/[microgram_C/microgram_Chl_ a)]. A value of 0.0 denotea no change in Chl_b:Chl_a ratio.
mxChlB == 0.0000d+00 0.0000d+00 0.0000d+00 0.0000d+00

Maximum Chl_b:Chl_a ratio (microgram_Chl_b/microgram_Chl_a). A value of 0.0 denotes no Chl_b.

b_ChlB == 0.0000d+00 0.0000d+00 0.0000d+00 0.0000d+00
  • Rate of change in the Chl_c:Chl_a ratio [(microgram_Chl_c/microgram_Chl_a)/(microgram_C/microgram_Chl_a)]. A value of 0.0 denotes no change in Chl_c:Chl_a ratio.
mxChlC == -1.3600d-03 -1.2000d-03 0.0000d+00 0.0000d+00
  • Maximum Chl_c:Chl_a ratio (microgram_Chl_c/microgram_Chl_a). A value of 0.0 denotes no Chl_c.
b_ChlC == 3.4000d-01 3.4000d-01 5.6000d-02 0.0000d+00
  • Rate of change in the PSC:Chl_a ratio [(microgram_PSC/microgram_Chl_a)/microgram_C/microgram_Chl_a)]. A value of 0.0 denotes no change in PSC:Chl_a ratio.
mxPSC == -1.2000d-02 -1.0400d-02 0.0000d+00 0.0000d+00
  • Maximum PSC:Chl_a ratio (microgram_PSC/microgram_Chl_a). A value of 0.0 denotes no Photosynthetic Caroteniods.
b_PSC == 2.0000d+00 2.0000d+00 1.1060d+00 0.0000d+00
  • Rate of change in the PPC:Chl_a ratio [(microgram_PPC/microgram_Chl_a)/(microgram_C/microgram_Chl_ a)]. A value of 0.0 denotes no change in PPC:Chl_a ratio.
mxPPC == 0.0000d+00 0.0000d+00 1.8000d-03 9.0000d-03
  • Maximum PPC:Chl_a ratio (microgram_Chl_c/microgram_Chl_a). A value of 0.0 denotes no Photoprotective Caroteniods.
b_PPC == 1.0000d-01 1.0000d-01 1.6000d-01 3.0000d-01
  • Rate of change in the LPUb:Chl_a ratio [(microgram_LPUb/microgram_Chl_a)/(microgram_C/microgram_Chl_a)]. A value of 0.0 denotes no change in LPUb:Chl_a ratio.
mxLPUb == 0.0000d+00 0.0000d+00 0.0000d+00 0.0000d+00
  • Maximum LPUb:Chl_a ratio (migrogram_HPUb/microgram_Chl_a). A value of 0.0 denotes no LPUb.
b_LPUb == 0.0000d+00 0.0000d+00 0.0000d+00 0.0000d+00
  • Rate of change in the HPUb:Chl_a ratio [(microgram_HPUb/microgram_Chl_a)/(microgram_C/microgram_Chl_a)]. A value of 0.0 denotes no change in HPUb:Chl_a ratio.
mxHPUb == 0.0000d+00 0.0000d+00 0.0000d+00 -1.3000d-01
  • Maximum HPUb:Chl_a ratio (microgram_HPUb/microgram_Chl_a). A value of 0.0 denotes no HPUb.
b_HPUb == 0.0000d+00 0.0000d+00 0.0000d+00 2.0000d+01
  • Proportion of grazing stress that is apportioned to DOM (nondimensional).
FecDOC == 3.3330d-01 3.3330d-01 3.3330d-01 4.1670d-01
  • Proportion of grazing stress that is apportioned to fecal (nondimensional).
FecPEL == 3*1.6670d-01 8.3350d-02 3*1.6670d-01 8.3350d-02
  • Proportion of grazing stress that is recycled (nondimensional).
FecCYC == 3.3330d-01 3.3330d-01 3.3330d-01 4.1660d-01
  • Proportion of daily production that is lost to excretion (nondimensional)
ExALG == 5.0000d-03 5.0000d-03 5.0000d-03 5.0000d-03
  • Phytoplankton sinking speed (meters/day)
WS == 0.0000d+00 0.0000d+00 0.0000d+00 0.0000d+00
  • Phytoplankton grazing parameter (nondimensional).
HsGRZ == 0.0100d+00 0.0100d+00 0.0100d+00 0.0100d+00
  • Refuge Phytoplankton population (micromole_C/liter)
MinRefuge == 2.0000d-02 2.0000d-02 2.0000d-02 2.0000d-02
  • Maximum Refuge Phytoplankton depth (meters)
RefugeDep == 4.0000d+01 4.0000d+01 4.0000d+01 4.0000d+01
  • Normalized Volume factor (nondimensional). (1 micron diameter cell = 1).
Norm_Vol == 7.2398d+01 7.2398d+01 7.2398d+01 4.6370d+00
  • Normalized Surface Area factor (nondimensional). (1 micron diameter cell = 1).
Norm_Surf == 1.7361d+01 1.7361d+01 1.7361d+01 2.7781d+00
  • Half Saturation Constant for DOP uptake (micromole_DOP/liter).
HsDOP == 1.0000d-05 1.0000d-05 2.0000d+00 1.0000d-05
  • C:P ratio where DOP uptake begins (micromole_C/micromole_P). Values above maxC2pALG denote no DOP uptake.
C2pALKPHOS == 5.0000d+02 5.0000d+02 1.1000d+02 5.0000d+02
  • Half Saturation constant for DON uptake (micromole_DON/liter).
HsDON == 1.0000d-05 1.0000d-05 2.0000d+00 1.0000d-05
  • C:N ratio where DON uptake begins (micromole_C/micromole_N). Values above maxC2nALG denote no DOP uptake.
C2nNupDON == 5.0000d+02 5.0000d+02 1.4000d+01 5.0000d+02

Bacteria Group Parameters

  • Half saturation constant for bacteria DOC uptake (micromole_DOC/liter).
HsDOC_ba == 130.0d+00
  • Maximum 24 hour bacterial growth rate (1/day).
GtBAC_max == 2.0d+00
  • Bacteria temperature base for exponential response to temperature (Celsius).
BacTbase == 27.0d+0
  • Bacteria exponential temperature factor (1/Celsius).
BacTfac == 0.092d+00
  • Carbon to Nitrogen ratio of Bacteria (micromole_C/micromole_N).
C2nBAC == 5.0d+00
  • Carbon to Phosphorus ratio of Bacteria (micromole_C/micromole_P).
C2pBAC == 60.0d+00
  • Carbon to Iron ratio of Bacteria (micromole_C/micromole_Fe).
C2FeBAC == 1000.0d+00

Proportion of bacteria grazing stress that is apportioned to DOM (nondimensional).

BacDOC == 4.583d-01
  • Proportion of bacteria grazing stress that is apportioned to fecal (nondimensional).
BacPEL == 8.340d-02
  • Proportion of bacteria grazing stress that is recycled (nondimensional).
BacCYC == 4.583d-01
  • Bacterial recalcitrant carbon excretion as a proportion of uptake (nondimensional).
ExBAC_c == 4.0d-02
  • Bacterial recalcitrant excretion carbon to nitrogen ratio (micromole_C/micromole_N).
ExBacC2N == 15.0d0
  • Bacterial gross growth carbon efficiency (nondimensional).
Bac_Ceff == 0.3d0
  • Maximum nitrification rate (1/day).
RtNIT == 0.4d0
  • Half-saturation constant for bacterial nitrification (micromole_NH4/liter).
HsNIT == 0.1d0
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